PhageTerm error

Question

[NIkita]

HI!

When i try to find termini in my phage genome, i get such problem

My input:

/home/nikita/Documents/test_task/ptv-py3_release_1_light/PhageTerm.py -f sub.R1.fq -p sub.R2.fq -r pilon_checked.fasta --report_title putative_phage

My output:

Traceback (most recent call last):
  File "/home/nikita/Documents/test_task/ptv-py3_release_1_light/PhageTerm.py", line 327, in <module>
    main()
    ~~~~^^
  File "/home/nikita/Documents/test_task/ptv-py3_release_1_light/PhageTerm.py", line 290, in main
    multiReport = CreateReport(phagename=DC,
                               draw=draw,
                               multi=1,
                               multiReport=multiReport,
                               **stat_dict)
  File "/home/nikita/Documents/test_task/ptv-py3_release_1_light/_modules/functions_PhageTerm.py", line 954, in CreateReport
    figP_norm = GraphCov(termini_coverage_norm_close, picMaxPlus_norm_close[:1], picMaxMinus_norm_close[:1], phagename + "-norm", 1, draw)
  File "/home/nikita/Documents/test_task/ptv-py3_release_1_light/_modules/functions_PhageTerm.py", line 408, in GraphCov
    axes.axhline(y=0.5, xmin=0, xmax=x_strandplus, color='grey', linestyle='dashed', linewidth=1.5)
    ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 809, in axhline
    self.add_line(l)
    ~~~~~~~~~~~~~^^^
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/axes/_base.py", line 2407, in add_line
    self._update_line_limits(line)
    ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/axes/_base.py", line 2430, in _update_line_limits
    path = line.get_path()
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/lines.py", line 1052, in get_path
    self.recache()
    ~~~~~~~~~~~~^^
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/lines.py", line 689, in recache
    x = _to_unmasked_float_array(xconv).ravel()
        ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
  File "/home/nikita/.conda/envs/ngs/lib/python3.13/site-packages/matplotlib/cbook.py", line 1355, in _to_unmasked_float_array
    return np.asarray(x, float)
           ~~~~~~~~~~^^^^^^^^^^
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part.

AI cant help me:( I did QC, fastp, seqtk, SPAdes and Pilon. What should i do? Thanks!

[GenoMax]

Is python v.3.x default python on your machine?

It looks like someone else had reported an identical error last year ( https://sourceforge.net/p/phageterm/discussion/general/thread/f078b7a3ec/ ) which remains unaddressed.